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Yorodumi- PDB-1ern: NATIVE STRUCTURE OF THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ern | ||||||
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Title | NATIVE STRUCTURE OF THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] | ||||||
Components | PROTEIN (ERYTHROPOIETIN RECEPTOR) | ||||||
Keywords | CYTOKINE / ERYTHROPOIETIN RECEPTOR / SIGNAL TRANSDUCTION / CYTOKINE RECEPTOR CLASS 1 | ||||||
Function / homology | Function and homology information erythropoietin receptor activity / erythropoietin-mediated signaling pathway / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development ...erythropoietin receptor activity / erythropoietin-mediated signaling pathway / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway / heart development / nuclear speck / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Livnah, O. / Stura, E.A. / Wilson, I.A. | ||||||
Citation | Journal: Science / Year: 1999 Title: Crystallographic evidence for preformed dimers of erythropoietin receptor before ligand activation. Authors: Livnah, O. / Stura, E.A. / Middleton, S.A. / Johnson, D.L. / Jolliffe, L.K. / Wilson, I.A. #1: Journal: Science / Year: 1996 Title: Functional Mimicry of a Protein Hormone by a Peptide Agonist: The Epo Receptor Complex at 2.8 A Authors: Livnah, O. / Stura, E.A. / Johnson, D.L. / Middleton, S.A. / Mulcahy, L.S. / Wrighton, N.C. / Dower, W.J. / Jolliffe, L.K. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ern.cif.gz | 93 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ern.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ern.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ern_validation.pdf.gz | 375.2 KB | Display | wwPDB validaton report |
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Full document | 1ern_full_validation.pdf.gz | 396 KB | Display | |
Data in XML | 1ern_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1ern_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/1ern ftp://data.pdbj.org/pub/pdb/validation_reports/er/1ern | HTTPS FTP |
-Related structure data
Related structure data | 1ebpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23511.660 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P19235 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.2 % | |||||||||||||||
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Crystal grow | pH: 7.7 / Details: pH 7.7 | |||||||||||||||
Crystal grow | *PLUS Temperature: 22.5 ℃ / pH: 7.8 / Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 14951 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rsym value: 0.059 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.28 / % possible all: 97 |
Reflection | *PLUS Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 97 % / Rmerge(I) obs: 0.28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EBP Resolution: 2.4→50 Å / Cross valid method: R-FREE / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.216 / Rfactor Rwork: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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